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31509b75280eeab0410ae952967a97a8c4e896e8
lammps/src/delete_atoms.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "delete_atoms.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "group.h"
#include "region.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
#include <map>
using namespace LAMMPS_NS;
// allocate space for static class variable
DeleteAtoms *DeleteAtoms::cptr;
/* ---------------------------------------------------------------------- */
DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void DeleteAtoms::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Delete_atoms command before simulation box is defined");
if (narg < 1) error->all(FLERR,"Illegal delete_atoms command");
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use delete_atoms unless atoms have IDs");
// store state before delete
bigint natoms_previous = atom->natoms;
bigint nbonds_previous = atom->nbonds;
bigint nangles_previous = atom->nangles;
bigint ndihedrals_previous = atom->ndihedrals;
bigint nimpropers_previous = atom->nimpropers;
// delete the atoms
if (strcmp(arg[0],"group") == 0) delete_group(narg,arg);
else if (strcmp(arg[0],"region") == 0) delete_region(narg,arg);
else if (strcmp(arg[0],"overlap") == 0) delete_overlap(narg,arg);
else if (strcmp(arg[0],"porosity") == 0) delete_porosity(narg,arg);
else error->all(FLERR,"Illegal delete_atoms command");
if (mol_flag) delete_molecule();
// delete local atoms flagged in dlist
// reset nlocal
AtomVec *avec = atom->avec;
int nlocal = atom->nlocal;
int i = 0;
while (i < nlocal) {
if (dlist[i]) {
avec->copy(nlocal-1,i,1);
dlist[i] = dlist[nlocal-1];
nlocal--;
} else i++;
}
atom->nlocal = nlocal;
memory->destroy(dlist);
// if non-molecular system and compress flag set,
// reset atom tags to be contiguous
// set all atom IDs to 0, call tag_extend()
if (atom->molecular == 0 && compress_flag) {
tagint *tag = atom->tag;
for (i = 0; i < nlocal; i++) tag[i] = 0;
atom->tag_extend();
}
// reset atom->natoms and also topology counts
// reset atom->map if it exists
// set nghost to 0 so old ghosts of deleted atoms won't be mapped
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
recount_topology();
// print before and after atom and topology counts
bigint ndelete = natoms_previous - atom->natoms;
bigint ndelete_bonds = nbonds_previous - atom->nbonds;
bigint ndelete_angles = nangles_previous - atom->nangles;
bigint ndelete_dihedrals = ndihedrals_previous - atom->ndihedrals;
bigint ndelete_impropers = nimpropers_previous - atom->nimpropers;
if (comm->me == 0) {
if (screen) {
fprintf(screen,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
if (mol_flag) {
if (nbonds_previous)
fprintf(screen,"Deleted " BIGINT_FORMAT
" bonds, new total = " BIGINT_FORMAT "\n",
ndelete_bonds,atom->nbonds);
if (nangles_previous)
fprintf(screen,"Deleted " BIGINT_FORMAT
" angles, new total = " BIGINT_FORMAT "\n",
ndelete_angles,atom->nangles);
if (ndihedrals_previous)
fprintf(screen,"Deleted " BIGINT_FORMAT
" dihedrals, new total = " BIGINT_FORMAT "\n",
ndelete_dihedrals,atom->ndihedrals);
if (nimpropers_previous)
fprintf(screen,"Deleted " BIGINT_FORMAT
" impropers, new total = " BIGINT_FORMAT "\n",
ndelete_impropers,atom->nimpropers);
}
}
if (logfile) {
fprintf(logfile,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
if (mol_flag) {
if (nbonds_previous)
fprintf(logfile,"Deleted " BIGINT_FORMAT
" bonds, new total = " BIGINT_FORMAT "\n",
ndelete_bonds,atom->nbonds);
if (nangles_previous)
fprintf(logfile,"Deleted " BIGINT_FORMAT
" angles, new total = " BIGINT_FORMAT "\n",
ndelete_angles,atom->nangles);
if (ndihedrals_previous)
fprintf(logfile,"Deleted " BIGINT_FORMAT
" dihedrals, new total = " BIGINT_FORMAT "\n",
ndelete_dihedrals,atom->ndihedrals);
if (nimpropers_previous)
fprintf(logfile,"Deleted " BIGINT_FORMAT
" impropers, new total = " BIGINT_FORMAT "\n",
ndelete_impropers,atom->nimpropers);
}
}
}
}
/* ----------------------------------------------------------------------
delete all atoms in group, group will still exist
------------------------------------------------------------------------- */
void DeleteAtoms::delete_group(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal delete_atoms command");
int igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find delete_atoms group ID");
options(narg-2,&arg[2]);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
int *mask = atom->mask;
int groupbit = group->bitmask[igroup];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
delete all atoms in region
------------------------------------------------------------------------- */
void DeleteAtoms::delete_region(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal delete_atoms command");
int iregion = domain->find_region(arg[1]);
if (iregion == -1) error->all(FLERR,"Could not find delete_atoms region ID");
domain->regions[iregion]->prematch();
options(narg-2,&arg[2]);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
double **x = atom->x;
for (int i = 0; i < nlocal; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
delete atoms so there are no pairs within cutoff
which atoms are deleted depends on ordering of atoms within proc
deletions can vary with processor count
no guarantee that minimium number of atoms will be deleted
------------------------------------------------------------------------- */
void DeleteAtoms::delete_overlap(int narg, char **arg)
{
if (narg < 4) error->all(FLERR,"Illegal delete_atoms command");
// read args
double cut = force->numeric(FLERR,arg[1]);
double cutsq = cut*cut;
int igroup1 = group->find(arg[2]);
int igroup2 = group->find(arg[3]);
if (igroup1 < 0 || igroup2 < 0)
error->all(FLERR,"Could not find delete_atoms group ID");
options(narg-4,&arg[4]);
int group1bit = group->bitmask[igroup1];
int group2bit = group->bitmask[igroup2];
if (comm->me == 0 && screen)
fprintf(screen,"System init for delete_atoms ...\n");
// request a full neighbor list for use by this command
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->command = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
// init entire system since comm->borders and neighbor->build is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
lmp->init();
// error check on cutoff
// if no pair style, neighbor list will be empty
if (force->pair == NULL)
error->all(FLERR,"Delete_atoms requires a pair style be defined");
if (cut > neighbor->cutneighmax)
error->all(FLERR,"Delete_atoms cutoff > neighbor cutoff");
// setup domain, communication and neighboring
// acquire ghosts and build standard neighbor lists
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
// build neighbor list this command needs based on earlier request
NeighList *list = neighbor->lists[irequest];
neighbor->build_one(irequest);
// allocate and initialize deletion list
// must be after exchange potentially changes nlocal
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
// double loop over owned atoms and their full neighbor list
// at end of loop, there are no more overlaps
// only ever delete owned atom I, never J even if owned
tagint *tag = atom->tag;
int *mask = atom->mask;
double **x = atom->x;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int i,j,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
double factor_lj,factor_coul;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
// if both weighting factors are 0, skip this pair
// could be 0 and still be in neigh list for long-range Coulombics
// want consistency with non-charged pairs which wouldn't be in list
if (factor_lj == 0.0 && factor_coul == 0.0) continue;
// only consider deletion if I,J distance < cutoff
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq >= cutsq) continue;
// only consider deletion if I,J are in groups 1,2 respectively
// true whether J is owned or ghost atom
if (!(mask[i] & group1bit)) continue;
if (!(mask[j] & group2bit)) continue;
// J is owned atom:
// delete atom I if atom J has not already been deleted
// J is ghost atom:
// delete atom I if J,I is not a candidate deletion pair
// due to being in groups 1,2 respectively
// if they are candidate pair, then either:
// another proc owns J and could delete J
// J is a ghost of another of my owned atoms, and I could delete J
// test on tags of I,J insures that only I or J is deleted
if (j < nlocal) {
if (dlist[j]) continue;
} else if ((mask[i] & group2bit) && (mask[j] & group1bit)) {
if (tag[i] > tag[j]) continue;
}
dlist[i] = 1;
break;
}
}
}
/* ----------------------------------------------------------------------
create porosity by deleting atoms in a specified region
------------------------------------------------------------------------- */
void DeleteAtoms::delete_porosity(int narg, char **arg)
{
if (narg < 4) error->all(FLERR,"Illegal delete_atoms command");
int iregion = domain->find_region(arg[1]);
if (iregion == -1) error->all(FLERR,"Could not find delete_atoms region ID");
domain->regions[iregion]->prematch();
double porosity_fraction = force->numeric(FLERR,arg[2]);
int seed = force->inumeric(FLERR,arg[3]);
options(narg-4,&arg[4]);
RanMars *random = new RanMars(lmp,seed + comm->me);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
double **x = atom->x;
for (int i = 0; i < nlocal; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
if (random->uniform() <= porosity_fraction) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
delete atoms in molecules with any deletions
use dlist marked with atom deletions, and mark additional atoms
do not include molID = 0
------------------------------------------------------------------------- */
void DeleteAtoms::delete_molecule()
{
// hash = unique molecule IDs from which I deleted atoms
hash = new std::map<tagint,int>();
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (molecule[i] == 0) continue;
if (dlist[i] && hash->find(molecule[i]) == hash->end())
(*hash)[molecule[i]] = 1;
}
// list = set of unique molecule IDs from which I deleted atoms
// pass list to all other procs via comm->ring()
int n = hash->size();
tagint *list;
memory->create(list,n,"delete_atoms:list");
n = 0;
std::map<tagint,int>::iterator pos;
for (pos = hash->begin(); pos != hash->end(); ++pos) list[n++] = pos->first;
cptr = this;
comm->ring(n,sizeof(tagint),list,1,molring,NULL);
delete hash;
memory->destroy(list);
}
/* ----------------------------------------------------------------------
update bond,angle,etc counts
different for atom->molecular = 1 or 2
------------------------------------------------------------------------- */
void DeleteAtoms::recount_topology()
{
bigint nbonds = 0;
bigint nangles = 0;
bigint ndihedrals = 0;
bigint nimpropers = 0;
if (atom->molecular == 1) {
int *num_bond = atom->num_bond;
int *num_angle = atom->num_angle;
int *num_dihedral = atom->num_dihedral;
int *num_improper = atom->num_improper;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (num_bond) nbonds += num_bond[i];
if (num_angle) nangles += num_angle[i];
if (num_dihedral) ndihedrals += num_dihedral[i];
if (num_improper) nimpropers += num_improper[i];
}
} else if (atom->molecular == 2) {
Molecule **onemols = atom->avec->onemols;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
int nlocal = atom->nlocal;
int imol,iatom;
for (int i = 0; i < nlocal; i++) {
imol = molindex[i];
iatom = molatom[i];
nbonds += onemols[imol]->num_bond[iatom];
nangles += onemols[imol]->num_angle[iatom];
ndihedrals += onemols[imol]->num_dihedral[iatom];
nimpropers += onemols[imol]->num_improper[iatom];
}
}
if (atom->avec->bonds_allow) {
MPI_Allreduce(&nbonds,&atom->nbonds,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (!force->newton_bond) atom->nbonds /= 2;
}
if (atom->avec->angles_allow) {
MPI_Allreduce(&nangles,&atom->nangles,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (!force->newton_bond) atom->nangles /= 3;
}
if (atom->avec->dihedrals_allow) {
MPI_Allreduce(&ndihedrals,&atom->ndihedrals,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (!force->newton_bond) atom->ndihedrals /= 4;
}
if (atom->avec->impropers_allow) {
MPI_Allreduce(&nimpropers,&atom->nimpropers,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (!force->newton_bond) atom->nimpropers /= 4;
}
}
/* ----------------------------------------------------------------------
callback from comm->ring()
cbuf = list of N molecule IDs, put them in hash
loop over my atoms, if matches molecule ID in hash, delete that atom
------------------------------------------------------------------------- */
void DeleteAtoms::molring(int n, char *cbuf)
{
tagint *list = (tagint *) cbuf;
int *dlist = cptr->dlist;
std::map<tagint,int> *hash = cptr->hash;
int nlocal = cptr->atom->nlocal;
tagint *molecule = cptr->atom->molecule;
hash->clear();
for (int i = 0; i < n; i++) (*hash)[list[i]] = 1;
for (int i = 0; i < nlocal; i++)
if (hash->find(molecule[i]) != hash->end()) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
process command options
------------------------------------------------------------------------- */
void DeleteAtoms::options(int narg, char **arg)
{
compress_flag = 1;
mol_flag = 0;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"compress") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal delete_atoms command");
if (strcmp(arg[iarg+1],"yes") == 0) compress_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) compress_flag = 0;
else error->all(FLERR,"Illegal delete_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal delete_atoms command");
if (atom->molecular == 0)
error->all(FLERR,"Cannot delete_atoms mol yes for "
"non-molecular systems");
if (strcmp(arg[iarg+1],"yes") == 0) mol_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) mol_flag = 0;
else error->all(FLERR,"Illegal delete_atoms command");
iarg += 2;
} else error->all(FLERR,"Illegal delete_atoms command");
}
}
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